Abstract Secreted and cell-surface-localized Immunoglobulin Superfamily proteins (?extracellular IgSFs?) are important class of proteins, which includes proven targets for the treatment of autoimmune diseases and cancer. The human proteome contains ~500 extracellular IgSFs, the largest superfamily of cell surface molecules that contribute to the regulation of innate and adaptive immunity, via specific IgSF:IgSF interactions at the ?Immune Synapse? formed between antigen-presenting cells and T-cells. Our long-term goal is to understand the molecular basis of interactions in the immune synapse. This requires the mapping of receptor-ligand interactions among the vast number of un-annotated IgSFs, and to gain insight about the specificity of these interactions. Subsequently, we plan to leverage our newly-gained insights into redesigning protein interfaces for specificity, both in order to generate new reagents that in turn can further interrogate the regulatory mechanisms within the immune synapse, and to establish potential new drug leads that can rationally modulate the immune response in diseases. In this application we will further develop our protein design-aided pharmacophore approach, ProtLID and utilize it for identifying cognate partners in the immune synapse, and for designing specific interfaces. We will also explore to synergisticly combine computational and experimental protein engineering techniques. We will develop an interdisciplinary approach where computationally designed, residue-based pharmacophore descriptions of the receptor-ligand interface are used to direct the library design in subsequent phage display experiments, allowing for the effective exploration of engineered constructs. All our computational results will be followed up with in vitro biochemical and cell-based experimental validation. These studies will directly expand the current knowledgebase of receptor-ligand pairs in the immune synapse and yield mutant molecules, with altered affinities and selectivities for therapeutic applications.